Variant Calling

Column

Overview

  • GATK4 best practices
  • Filtering:
    • Site level:
      • bi-allelic SNPs
      • 95% truth sensitivity (VQSR)
    • Genotype level (min 1/6 groups, min 20/25 samples):
      • min DP: 4
      • min GQ: 20
      • max DP: 77 (mean DP + 4*SD)

Number of Variants

variable raw site_filtered gt_filtered
TOTAL_SNPS 16,643,754.00 9,115,052.00 7,064,770.00
NUM_IN_DB_SNP 12,117,419.00 8,486,322.00 6,621,301.00
NOVEL_SNPS 4,526,335.00 628,730.00 443,469.00
PCT_DBSNP 0.73 0.93 0.94
DBSNP_TITV 1.94 2.07 2.19
NOVEL_TITV 1.07 1.53 1.64
TOTAL_INDELS 3,454,237.00 0.00 0.00
TOTAL_MULTIALLELIC_SNPS 856,605.00 0.00 0.00

Column

Per sample SNPs

SNPs per population (max 5 out of 25 missing)

SNP Annotations

LDD & SFS

Column

Allele frequency state per population

LD Decay

Column

Alternative Allele Frequency Distribution

Minor Allele Frequency Distribution

Diversity

Population Structure

Column

PC1 - PC2

PC2 - PC3

PC3 - PC4

PC4 - PC5

PC5 - PC6

Column

Hieratchical Clustering

Admixture

Admixture detailed

Column

K2

K3

K4

Column

K5

K6

Divergent Signatures

Directional Signatures